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H B Jenson

Publications and source records attributed to H B Jenson.

14 recordsLinked to original sources
PubMed1989

A dedicated database program for cataloging recombinant clones and other laboratory products of molecular biology technology.

A novel computer database program dedicated to storing, cataloging, and accessing information about recombinant clones and libraries has been developed for the IBM (or compatible) personal computer. This program, named CLONES, also stores information about bacterial strains and plasmid and bacteriophage vectors used in molecular biology. The advantages of this method are improved organization of data, fast and easy assimilation of new data, automatic association of new data with existing data, and rapid retrieval of desired records using search criteria specified by the user. Individual records are indexed in the database using B-trees, which automatically index new entries and expedite later access. The use of multiple windows, pull-down menus, scrolling pick-lists, and field-input techniques make the program intuitive to understand and easy to use. Daughter databases can be created to include all records of a particular type, or only those records matching user-specified search criteria. Separate databases can also be merged into a larger database. This computer program provides an easy-to-use and accurate means to organize, maintain, access, and share information about recombinant clones and other laboratory products of molecular biology technology.

Database Management Systems↗
PubMed1988

Polymorphisms of the region of the Epstein-Barr virus genome which disrupts latency.

The nucleotide sequence of the portion of naturally occurring defective EBV (HR-1) DNA (designated het DNA) which is responsible for disruption of EBV latency has been determined and compared with the regions of the standard HR-1 viral genome from which it was derived. This rearranged 2.7-kbp DNA fragment represented an apparently nonhomologous recombination between sequences found in the BamHI W and BamHI Z fragments of the standard HR-1 genome. Only one intact open reading frame, comparable to standard HR-1 BZLF1, was present within this 2.7 kbp. No new open reading frames were created by the recombination. The BZLF1 sequence and predicted polypeptide products of standard HR-1 and het DNA were compared to B95-8 EBV. If an unspliced version of BZLF1 is used, the carboxy end of the BZLF1 polypeptides would differ considerably, principally due to an identical 28-bp insertion in both standard HR-1 and het BZLF1 relative to B95-8. However, if both virus strains use the same mRNA splicing strategy, the BZLF1 products from HR-1 and B95-8 would be similar, though distinguished by seventeen 1-bp differences which would result in nine amino acid changes. Both unspliced and spliced versions of het BZLF1 had five amino acid changes by comparison to standard HR-1 BZLF1. Differences in predicted secondary structure were found, consistent with dissimilar electrophoretic mobility of the polypeptide products. The amino acid differences between the BZLF1 polypeptide products of HR-1, het DNA, and B95-8 virus are all compatible with the creation of a protein which would function similarly to disrupt EBV latency. The differences in these polypeptides may account for some of the variation in the level of biologic activity of the BZLF1 products of different EBV strains. However, the major difference in activity between standard HR-1 and HR-1 het virus to disrupt EBV latency appears to be due to up-regulation of expression of het BZLF1 due to juxtaposition of BamHI W sequences upstream of het BZLF1.

Amino Acid Sequence↗
PubMed1987

Two computer programs for rapid entry of DNA sequence data.

Two computer programs for the IBM personal computer are described for rapid and accurate entry of DNA sequence data. The DNA sequence files produced can be used directly by the DNA sequence manipulation programs by R. Staden (the DataBase system), the University of Wisconsin Genetics Computer Group, DNASTAR, or D.Mount. The first program, DIGISEQ, utilizes a sonic digitizer for semi-automation of sequence entry. To enter the DNA sequence each band of a gel reading is touched by the stylus of the sonic digitizer. DIGISEQ corrects for both changes in lane width and lane curvature. The algorithm is extremely efficient and rarely requires re-entering the centers of the lanes. The second program, TYPESEQ, uses only the keyboard for input. The keyboard is reconfigured to place nucleotides and ambiguity codes under the fingers of one hand, corresponding to the order of the nucleotides on the gel defined by the user. Both programs produce individual tones for each nucleotide, and certain ambiguity codes. This verifies input of the correct nucleotide or ambiguity code, and thus eliminates the need to visually check the screen display during sequence entry.

Base Sequence↗
PubMed1987

Sequences of the Epstein-Barr Virus (EBV) large internal repeat form the center of a 16-kilobase-pair palindrome of EBV (P3HR-1) heterogeneous DNA.

We have previously characterized several genomic rearrangements of Epstein-Barr virus (EBV) DNA contained in one of the defective EBV genomes harbored by the P3HR-1 (HR-1) line (H. B. Jenson, M. S. Rabson, and G. Miller, J. Virol. 58:475-486, 1986). One recombinant clone of heterogeneous DNA (het DNA) from this defective genome is an EcoRI fragment of 16 kilobase pairs (kbp) which is a palindrome. DNA digestion fragments specific for the center of this palindrome were present in cells which contained het DNA but not in cells which lacked het DNA. Thus, the palindrome was not an artifact of DNA cloning. The organization of the center of this palindrome was studied by DNA sequencing. The comparable region of the parental HR-1 genome was also studied by DNA sequencing. The central 3,495 base pairs (bp) of the palindrome were composed of sequences derived exclusively from internal repeat 1 of EBV, represented by BamHI W fragment. At each end of the central 3,495 hp was a symmetrical recombination with sequences of BamHI-Z, located more than 50 kbp away on the standard EBV genome. The central 3,495 bp were composed of an unduplicated 341 bp flanked by two perfect palindromic repeats of 1,577 bp. The 341-bp unique region was a portion of a 387-bp region of standard HR-1 BamHI-W which was identical to the central 387 bp of the palindrome. This central 387-bp region contained numerous stretches of dyad symmetry capable of forming a large stem-and-loop structure. The palindromic rearrangement had created two novel open reading frames in het DNA derived from standard HR-1 BamHI-W sequences. These two het DNA open reading frames had different amino termini but identical carboxy termini derived from the large open reading frame in standard HR-1 BamHI-W (HR-1 BWRF1). The BamHI-W sequences found in het DNA did not include either the TATA box of standard HR-1 BamHI-W or the exons which are present in the potentially polycistronic latent mRNAs encoding EBV nuclear antigens. These marked alterations in genomic structure may relate to the unique biologic properties of virus stocks containing het DNA by creation of new polypeptides or by formation or deletion of regulatory or functional signals.

Base Sequence↗
PubMed1987

Congenital cytomegalovirus infection with osteolytic lesions: use of DNA hybridization in diagnosis.

A case of congenital cytomegalovirus (CMV) infection with long-bone lesions is presented. The bone lesions consisted of broad regions of generalized osteopenia with irregular fragmentation and spiculization at the zone of provisional calcification. Diagnosis of CMV infection was made by DNA spot hybridization of the urine sediment to DNA from the Towne strain of CMV, demonstrating the usefulness of DNA hybridization for identification of CMV in clinical specimens. Bone lesions associated with congenital CMV infection are useful early clues to diagnosis but can be indistinguishable from those of congenital rubella syndrome.

Bone Diseases, Metabolic↗
PubMed1986

Palindromic structure and polypeptide expression of 36 kilobase pairs of heterogeneous Epstein-Barr virus (P3HR-1) DNA.

Among the Epstein-Barr virions (EBV) produced by the P3HR-1 (HR-1) cell line are a defective subpopulation with rearranged viral DNA designated heterogeneous DNA (het DNA). These defective virions are responsible for the capacity of HR-1 virus to induce early antigen in Raji c cells and for trans activation of latent EBV in X50-7 cells. Virions with het DNA are independent replicons which pass horizontally from cell to cell rather than being partitioned vertically. We analyzed the structure and defined several polypeptide products of het DNA to understand these remarkable biologic properties. A 36-kilobase-pair (kbp) stretch of het DNA was cloned (as two EcoRI fragments of 20 and 16 kbp) from virions released from a cellular subclone of HR-1 cells. The unusual aspect of the 20-kbp fragment was the linkage of sequences of BamHI-M and BamHI-B', which are not adjacent on the standard EBV genome. The 16-kbp fragment was a palindrome in which at least two additional recombinations on each side of the palindrome had linked regions of the standard EBV genome which are not normally contiguous. The 20-kbp het DNA fragment was attached to at least one and possibly both ends of the 16-kbp het DNA fragment. We identified antigenic polypeptides produced in COS-1 cells after gene transfer of various cloned het DNA fragments. The 20-kbp fragment encoded a cytoplasmic antigen of about 95 kilodaltons (kDa). The 16-kbp fragment encoded antigens located in the nucleus, nuclear membrane, and cytoplasm. These were represented by several polypeptides, the most prominent of which were about 55, 52, and 36 kDa. The 36-kDa polypeptide was localized to a 2.7-kbp BamHI fragment which had homology to standard BamHI-W and BamHI-Z. Another polypeptide of 50 kDa found in the nucleus was mapped to the 7.1-kbp BamHI het DNA fragment which spans the EcoRI site linking the 20- and 16-kbp fragments of het DNA. Thus, HR-1 het DNA encodes several discrete polypeptide products, one or more of which could be responsible for the unusual biologic properties of the virus. The composition, regulation, and ultimately the expression of some of these products relative to standard EBV is probably altered by the genomic rearrangements of het DNA.

Animals↗